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Marijana Radonjic, PhD
ORGANIZING DATA TO
EMPOWER DECISION MAKING
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DATA
DECISION
INFORMATION
KNOWLEDGE
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NuGO week 2014Participant list(hard copy)
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Institute
Person
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In Marijana’s LinkedIn
Not (yet) in Marijana’s LinkedIn
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COMPLEXITY OF HEALTH FACTORS
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PEAK INTO THE FUTURE
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JAN FEB MAR APR MAY JUN
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FOOD - GENOMICS - HEALTH
LANDSCAPE
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BRIDGING FOOD AND HEALTH
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Ingredient GeneFooDB: 9,955 food
ingredients, 858 foods
HMDB: 4,025 associated
enzymes & transporters
Disease
UMLS: 8,521 diseasesDisgeNET: 13,828 associated genes & proteins
GeneticsBiomarkersMechanistic
EnzymesTransporters
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BRIDGING FOOD AND HEALTH
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Ingredient Gene
Disease
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FOOD - GENOMICS - HEALTH NETWORK
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Significance filter(Monte Carlo randomization
procedure p < 0.001)
Projection to disease-
ingredient space
Bipartitedisease-gene-ingredient
network
Disease-Ingredientnetwork
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Neoplasms
Metabolic syndrome
and complications
Mental disorders817 connected diseases316 connected ingredients1,961 disease-ingredient relations(p < 0.001)Network cluster coefficient = 0.42 (v.s. random graph ~0.006)
FOOD - GENOMICS - HEALTH
LANDSCAPE
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NETWORK RECONSTRUCTS DISEASE AND
INGREDIENTS CLASSES
Most or all topology based clusters (47/67 for diseases and 10/10 for ingredients) are significantly enriched with one or more predefined MeSH disease and/or HMDB chemical classes (p < 0.05).
Significant enrichment (p < 0.01)
Clusters enriched with main disease classes
Clusters enriched with main ingredient classes
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Raw data
GOING PERSONALIZED
Rs1234(A;A)
Rs1234(G;G)
Increased risk
Decreased risk
Disconnected information
Personal disease-ingredient network
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PERSONAL FOOD - GENOMICS - HEALTH
LANDSCAPE
Disease
Decreased risk
Increased risk
Mixed evidence
Linked to variant
Not linked to variant
Ingredient
AtherosclerosisCoronary diseaseHypertensionObesityDiabetesDementia
Cancers
PsychosisAutismMigrane disordersDepression‘as if’ personalityNicotine dependence
Cluster headacheHypertension
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NUTS – ATHEROSCLEROSIS ASSOCIATION
Disease
Increased risk
Linked to variant
Not linked to variant
Ingredient
Vegetables;Fruits;Herbs and Spices;Nuts;Cereals and cereal products;Pulses;Teas;Gourds;Coffee
CETP
Fats and oils
Herbs and Spices
Cocoa and cocoa products;Fats and oils
Cocoa and cocoa products;Fats and oils
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WHAT ELSE WILL BE AFFECTED?
Disease
Increased risk
Mixed evidence
Linked to variant
Ingredient
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FROM INGREDIENTS TO DIET
23andMe SNP profiles(11 individuals)
Whole foods for which their ingredients enriched in personal networks
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CHALLENGES AHEAD
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• From ingredients to diets: diets in genetics context
• Beyond genetics: involve broader phenotypic data (dietary
questionnaires, activity measurements, self monitoring devices,
medical history)
• Time resolved data (current status, future risk)
• Standardization of knowledge:
• Ontologies to map between resources
• Publish in structured format
• Add directionality of relations: from associations to causal
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MAKING DECISIONS
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Understand big picture beyond single SNP-
ingredient associations
Improve advice on dietary lifestyle
Develop healthy food
(Re)position existing product
What to eat to stay healthy?
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THANKS
Georg SummerPhD Student, co-supervised by Maastricht University / TNO / EdgeLeap
Thomas KelderEdgeLeap
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